title: Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.
abstract: FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut.
authors.affiliation: Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Myers
authors.forename: Huihuang
authors.initials: H
authors.lastname: Yan
authors.forename: Irene M
authors.initials: IM
authors.lastname: Ong
authors.forename: Dongjun
authors.initials: D
authors.lastname: Chung
authors.forename: Kun
authors.initials: K
authors.lastname: Liang
authors.forename: Frances
authors.initials: F
authors.lastname: Tran
authors.forename: Sündüz
authors.initials: S
authors.lastname: Keleş
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
authors.forename: Patricia J
authors.initials: PJ
authors.lastname: Kiley
mesh_terms: D000693:Anaerobiosis / Q000235:genetics*; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D007506:Iron-Sulfur Proteins / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; C060704:FNR protein, E coli; D007506:Iron-Sulfur Proteins; D014157:Transcription Factors